Data access including levels of access are described. Learners will be able to illustrate data access in terms of the FAIR Principles using companion terms including communications protocol and authentication. Learners will also be able to interpret the data usage licence associated with different data sets

Agenda

In this tutorial, we will cover:

1. Data access and the FAIR Principles
2. What is data access?
3. Types of data access
4. Data usage licence
5. Making sensitive data accessible
6. Useful resources

Data access and the FAIR Principles

Data access relates to the following 5 FAIR Principles (Table 4.1). We will discuss and signpost these in this episode.

Table 4.1: The 15 FAIR Guiding Principles. Principles relating to data access are highlighted in black.

What is data access?

Making data accessible means it can be made available to use by both humans and computers, though FAIR data does not necessarily mandate that all data is openly accessible and we discuss this in a minute.

As outlined in the Accessibility Principles (meta)data must be retrievable by their identifier using a standardised communication protocol (FAIR Principle A1) which is open, free and universally implementable (FAIR Principle A1.1).

A standardised communication protocol is something like http(s) or FTP that allows data to be requested and downloaded, for example, by clicking on a link on a webpage. Simply put, a protocol is a method that connects two computers and ensures secure data transfer. Web browsers such as Firefox and Chrome can use the http(s) communication protocol since it is universally implementable, open and free.

It is important to note that (meta)data access is not limited to humans clicking links on webpages. For a machine ‘user’, examples of accessing data include the use of an ‘application programming interface’ (API), and Unix command line, using wget and curl.

We mentioned above that FAIR data does not necessarily mandate open data. Commonly, this relates to controlled access, which is discussed later in this Episode, but in the exercise below we investigate a dataset that has been deleted where it has been previously accessible. FAIR states: “metadata are accessible even when the data are no longer available” (FAIR Principle A2) which is one of the few principles that relate solely to metadata (and not data). This means data can be deleted from its original online location at any time, but its original metadata must remain accessible. PIDs (usually connected through URLs) to the original data must remain live, though the record may, for example, change to display metadata only. This is useful where originally referenced data changes over time, or becomes obsolete or deprecated; a record of the original metadata, and where appropriate reasons for its removal, or redirection to updated records, provide a provenance trail from the original data, which may have been referenced, for example, in publications, where it is not possible to update the PID.

Question

The Protein Data Bank in Europe (PDBe) is a searchable repository of biological macromolecular structures. Please take a look at the following record that has been retired: 1ins. You will see that the crystal structure is no longer available, but what metadata is available?

Solution

Metadata includes the original citation, an explanation of why the record is no longer available and a redirection to the replacement entry.

Types of data access

Where restricted access is required (for example, sensitive data or data subject to intellectual property) generally only the recommended parts are restricted, whereas associated metadata and non-sensitive data are openly accessible. As part of the FAIR Principles, terms of access need to be stated, usually as part of a data licence (FAIR Principle R1.1). Remember, FAIR data is as open as possible, and as closed as necessary. Resources for working with sensitive data are given at the end of this Episode.

There are four types of data access as described in RDMkit:

Open access: Anyone can access the data, and use it for any purpose.

Registered access or authentication procedure: researchers are required to register and authenticate to have the right to access the data (login and password)

Controlled access or Data Access Committees (DACs): researchers will apply for access, and their application reviewed by a data access committee

Access upon request (not recommended): a researcher provides their contact details for access. Contact details should be provided in the metadata which will be publicly available.

Any access requiring login and password makes use of “[a protocol] allowing for an authentication and authorisation procedure, where necessary” (FAIR Principle A1.2). Commonly for authentication, a researcher will be assigned a unique ID, or the system may support sign-in with an ORCID ID, which is the case of many data repositories including Zenodo. In some cases, there may be an option to use a Google account or institutional email to sign in, and many infrastructures also support ‘single sign in’.

Data usage licence

A data usage licence describes the legal rights on how others use your data. When you publish your data, you should describe clearly in what capacity your data can be used.

There are many types of licences that can be used, including the MIT licence (for software) or the commonly used Creative Commons licences (a selectable collection of licences). These licences provide precise descriptions of the rights to data use, where the latter defines rights for sharing, adapting and commercialisation. Open access data usually carries the CC BY 4.0 or CC0 licence permitting open sharing and adaptation, even for commercial purposes. The licence is applied by adding the licence declaration to the data similar to this training page. Take a look at the banner at the bottom of this page. It states: Licensed under CC-BY 4.0 2018–2023 by The Carpentries.

Making sensitive data accessible

Controlled access is often afforded to sensitive data or commonly any data that could potentially harm, see RDMkit for a full definition.

Where access is granted, sensitive data is often de-identified, meaning that identifying (meta) data is removed or reassigned, leaving the analytics-appropriate component.

For example, a participant’s name can be removed from a questionnaire, and their home address can be substituted for the name of the town they live in. This anonymises the data since the participant can no longer be located. Note though that other information in the questionnaire could compromise this. If other data reveal that the participant won the town’s 10K road race in 2023, we could potentially identify the individual using the name of the town and an online search. If more information in the questionnaire states that the participant has a rare disease, we are broaching disclosure of sensitive, personal data.

Though people refer to anonymisation when de-identifying (meta)data, often they mean pseudonymisation. Data anonymisation and pseudonymisation are slightly different.

Data anonymisation is the process of irreversibly de-identifying personal data such that an individual cannot be identified by anyone, including the study team and the individual themselves. If data are anonymised, no one can link data back to the subject.

Pseudonymisation is more commonly used. It is a process where identifying-fields are replaced by artificial identifiers called pseudonyms or pseudonymised IDs. Commonly, a person’s name or medical ID will be replaced with a unique participant ID within the study. Pseudonymisation ensures no one can link data back to the individual, apart from nominated members of the study team who will be able to link pseudonyms to identifying information, such as medical records.

Question

Use RDMkit’s guidelines on sensitive data to familiarise yourself further on de-identification of data. What further training can you identify?

Solution

At the bottom of the page, under “Training”, useful resources are given. The TeSS training portal permits users to search for courses, events, videos and other learning material for data in the life sciences.

Useful resources

• More about Data Access and Sharing: RDMkit, FAIR Cookbook
• Definition and examples of Standardised Communication protocol using authentication: Australian Research Data Commons
• More about Data licensing: RDMkit, FAIR Cookbook
• The Creative Commons licences
• Working with sensitive data: EBI training

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Key points

• Data access is supported by standardised communication protocols allowing for authentication where appropriate.

• Metadata must be available even if data are deleted.

• Data usage licences are applied to (meta)data detailing terms of use.

• Sensitive data can be subject to restricted access and/or de-identification.

Frequently Asked Questions

Glossary

FAIR

Findable, Accessible, Interoperable, Reusable

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Citing this Tutorial

1. Robert Andrews, Nick Juty, Munazah Andrabi, Nicola Soranzo, Sara Morsy, Kellie Snow, Korneel Hens, Philippe Rocca-Serra, Laura Cooper, Xenia Perez Sitja, Andrew Mason, Branka Franicevic, Saskia Lawson-Tovey, Katarzyna Kamieniecka, Khaled Jum'ah, Krzysztof Poterlowicz, Access (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/fair/tutorials/fair-access/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{fair-fair-access,
author = "Robert Andrews and Nick Juty and Munazah Andrabi and Nicola Soranzo and Sara Morsy and Kellie Snow and Korneel Hens and Philippe Rocca-Serra and Laura Cooper and Xenia Perez Sitja and Andrew Mason and Branka Franicevic and Saskia Lawson-Tovey and Katarzyna Kamieniecka and Khaled Jum'ah and Krzysztof Poterlowicz",
	title = "Access (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/fair/tutorials/fair-access/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol} Computational Biology}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

DASH UK

This Fellowship was funded through the ELIXIR-UK DaSH project as part of the UKRI Innovation Scholars: Data Science Training in Health and Bioscience call (DaSH). (MR/V038966/1). The project aims to embed Research Data Management (RDM) know-how into UK universities and institutes by producing and delivering training in FAIR data stewardship using ELIXIR-UK knowledge and resources.

Go Further

Do you want to extend your knowledge? Follow one of our recommended follow-up trainings:

• tutorial Hands-on: Persistent Identifiers

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/fair/tutorials/fair-access/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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